glutamate measurement for MEGA-PRESS

[samuraimichelle.he]

i all, 

I just wondered whether there's any possibility to calculate the amount of glutamate from the output of Glx_A,  Glx_B,  Glx_C,  Glx_D (the co-edited Glx peak as the sum of 4 Lorentzians). 

My thought was using the frequency, line width, and amplitude(the fitted parameters) to calculate the areas, but I just a little bit confuse how to deal with it....

Thank you!

Xuanzi

[Martin Wilson]

Hi Xuanzi,

I would use the edit-off scans to measure glutamate, you can get these by averaging the odd (or even scans) depending on your sequence.

However, it looks like you have a pretty significant lipid signal so take care with interpretation.

Martin

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[Xuanzi He]

Hi Martin,

Thank you so much for the quick reply. I just wondered whether I conducted it correctly as following: 

I used all the default setting of MEGA-PRESS except altering dynamic averaging (WS) to be average even scan only while leaving dynamic averaging(W) as default.

But the result seems quite similar to the previous one, as no glu report but 4 different glx. I'm wondering whether I could use the PRESS setting for calculating glutamate since the MEGA-PRESS is a kinda of stimulation....

​

Thank you!

Xuanzi

[Felix Raschke]

Hi Xuanzi,

when you average even or odd scans only make sure you select PRESS as the pulse sequence and use the standard 1H brain basis set (not MEGA-PRESS).

best wishes

Felix

On Tuesday, February 17, 2015 at 11:37:57 PM UTC, samuraimichelle.he wrote:

Hi Martin,

Thank you so much for the quick reply. I just wondered whether I conducted it correctly as following: 

I used all the default setting of MEGA-PRESS except altering dynamic averaging (WS) to be average even scan only while leaving dynamic averaging(W) as default.

But the result seems quite similar to the previous one, as no glu report but 4 different glx. I'm wondering whether I could use the PRESS setting for calculating glutamate since the MEGA-PRESS is a kinda of stimulation....

​

Thank you!

Xuanzi

On Tue, Feb 17, 2015 at 4:22 AM, Martin Wilson <mar...@pipegrep.co.uk> wrote:

Hi Xuanzi,

I would use the edit-off scans to measure glutamate, you can get these by averaging the odd (or even scans) depending on your sequence.

However, it looks like you have a pretty significant lipid signal so take care with interpretation.

Martin

On 16 February 2015 at 20:07, samuraimichelle.he <samuraimi...@gmail.com> wrote:

i all, 

I just wondered whether there's any possibility to calculate the amount of glutamate from the output of Glx_A,  Glx_B,  Glx_C,  Glx_D (the co-edited Glx peak as the sum of 4 Lorentzians). 

My thought was using the frequency, line width, and amplitude(the fitted parameters) to calculate the areas, but I just a little bit confuse how to deal with it....

Thank you!

Xuanzi

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[Xuanzi He]

Thanks Felix! I really appreciate your help:) I just wondered may I clarify "standard 1H brain basis set" as the setting of PRESS as following:

ref 4.85  
start_pnt 10  
ref_signals 1h_naa  
int_basis braino  
w_conc 55556  
w_att 0.7

Thank you!

Xuanzi

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[Felix Raschke]

This are the parameters for a phantom, not really useable for in vivo data!

ref should be 4.68
int_basis needs to be 1h_brain or similar (not sure what the naming convention is - I use the TARQUIN GUI)

You may also want to adjust w_conc to match the rest of your analysis, 55556 is normally used for phantoms.

best wishes

Felix

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[Xuanzi He]

Hi Felix,

Thank you so much for the detailed reply. I used two different ways to calculate glutamate.

1. MEGA-PRESS average even only(edit-off) 

​

2. PRESS suppressed (act) & non-suppressed (ref) average all

​

Both measurements used the following parameters as you kindly suggested:

ref 4.68
start_pnt 10  
ref_signals 1h_naa  
int_basis 1h_brain
w_conc 35880 (Posterior Cingulate cortex, suppose to be white matter mainly)
w_att 0.7

I'm so confused why the results are so different, and I've attached the megapress & pair of press files I used, any suggestions or solutions would be really appreciated.

With much gratitude,

Xuanzi

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[Paul Mullins]

Hi Xuanzi,

it looks like your mega-press acquisition has a pretty substantial lipid contamination.  This will definitely impact your ability to get accurate measures for Glutamate (and NAA).  

Secondly it appears you do not have a water scan (ref) for the MEGA-PRESS data.  Is this correct?  If this is the case the amplitudes measured in the MEGA-PRESS data are not referenced, and are just raw amplitudes (Martin correct me if I'm wrong here). You could reference to Cr (Cr + PCr actually), but you would have to do the same for the PRESS data before you can make a comparison between the two acquisitions.  

You are using a really long echo time (144 ms at 3T) for Glutamate in your PRESS sequence.  Most people would suggest you use a shorter echo, either 30 or 40 ms with a PRESS sequence, or even shorter with something like STEAM or SPECIAL (I don't think the latter is available for Philips scanners yet).  You should be able to get a 10 ms TE with STEAM.  In addition, given that you are at 144 ms, the w_att parameter Felix suggested (actually the default parameter) does not correct properly for the increased T2 relaxation effects at longer echoes (although depending on what comparisons you are going to be making with the data, it may or may not be important - it will certainly be a problem if you are trying to compare to other studies).

Hope that helps to explain why the numbers are so different. 

Paul. 

[Felix Raschke]

I agree with Paul. It looks like you don't have a water reference file (should be a separate SDAT/SPAR pair), hence the low metabolite values.
As Paul said you could use the tCr from the OFF scans and calculate GABA/tCr.

If you get MEGA-PRESS data without lipid contamination (big hump between 2ppm-1ppm in your example) you should also be able to get a accurate Glutamate+Glutamin (or Glx) estimate from the edit OFF scans and you won't need the PRESS 144 data (unless you are looking for lactate). Example attached

best wishes

Felix

[Felix Raschke]

On Tuesday, February 24, 2015 at 10:16:47 AM UTC, Felix Raschke wrote:

I agree with Paul. It looks like you don't have a water reference file (should be a separate SDAT/SPAR pair), hence the low metabolite values.
As Paul said you could use the tCr from the OFF scans and calculate GABA/tCr.

If you get MEGA-PRESS data without lipid contamination (big hump between 2ppm-1ppm in your example) you should also be able to get a accurate Glutamate+Glutamin (or Glx) estimate from the edit OFF scans and you won't need the PRESS 144 data (unless you are looking for lactate). Example attached

best wishes

Felix

...

[Xuanzi He]

Hi Paul & Felix,

Thank you so much for the kindly reply. Correct I don't have a reference water scan for MEGA-PRESS.

Yes I used GABA/tCr as reference for my report, thanks for the reminding. I just wondered whether this result would still be influenced by the lipid contamination? 

For now I'm worried whether the possibility to produce reliable Glutamate results still exist using the current data? 

With thanks and much gratitude,

Xuanzi

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[caroline...@gmail.com]

Dear Martin, Paul, and Felix,

First, thank you Martin for developing this great tool (Tarquin), and all for the helpful discussion on resolving Glx in MEGA-PRESS spectra.

I have a quick question, which I hope will also close a loop in this discussion.  Like Xuanzi, I am hoping to measure Glx concentration in a set of MEGA-PRESS scans (obviously optimized for the detection of GABA).  I have a water reference scan and am able to clearly resolve Glx peaks in both the DIFFERENCE and OFF subspectra of my data.  I attach a screen shot which looks quite a lot like Felix's data posted in this thread on 2/24/15.

I note that you all recommend using Glx concentrations obtained from the OFF subspectra to estimate Glx.  My question is: why is this your recommendation?  I've noticed Glx concentrations from either Difference or OFF scans are reported in the literature.  

Many thanks!

Caroline

On Tuesday, February 24, 2015 at 9:07:44 PM UTC-5, samuraimichelle.he wrote:

Hi Paul & Felix,

Thank you so much for the kindly reply. Correct I don't have a reference water scan for MEGA-PRESS.

Yes I used GABA/tCr as reference for my report, thanks for the reminding. I just wondered whether this result would still be influenced by the lipid contamination? 

For now I'm worried whether the possibility to produce reliable Glutamate results still exist using the current data? 

With thanks and much gratitude,

Xuanzi

On Tue, Feb 24, 2015 at 5:18 AM, Felix Raschke <div...@gmail.com> wrote:

On Tuesday, February 24, 2015 at 10:16:47 AM UTC, Felix Raschke wrote:

I agree with Paul. It looks like you don't have a water reference file (should be a separate SDAT/SPAR pair), hence the low metabolite values.
As Paul said you could use the tCr from the OFF scans and calculate GABA/tCr.

If you get MEGA-PRESS data without lipid contamination (big hump between 2ppm-1ppm in your example) you should also be able to get a accurate Glutamate+Glutamin (or Glx) estimate from the edit OFF scans and you won't need the PRESS 144 data (unless you are looking for lactate). Example attached

best wishes

Felix

...

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[Martin Wilson]

Dear Caroline,

Good question. Whilst I can't speak for Paul and Felix, my person
preference for using the off spectra for measure Glu is as follows:

1. There is some reasonable evidence in the literature that approx
80ms PRESS is a good way to measure Glu
(http://www.ncbi.nlm.nih.gov/pubmed/15050596).
2. The misalignment of spectra and therefore motion/B0 stability
artefacts should be less of an issue when using just edit-off data.
3. I prefer to measure Glu from the resonances nearer to NAA as
chemical shift displacement is a concern when using the resonances
nearer to 4ppm. (this assumes your carrier frequency is set to be
close to NAA).

I should add that I don't think it is wrong to use edited data for Glu
measures, but you do have to take more care with chemical shift
displacement and subtraction artefacts.

Hope that helps,

Martin

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[Felix Raschke]

Hi Caroline,

I think that is a really good question. I had a look at a (LCModel) fit of GABA MEGA-PRESS data using an simulated basis set (should also work with TARQUIN - you can get it here: http://purcell.healthsciences.purdue.edu/mrslab/downloads.htm) rather than the default TARQUIN fit using several lineshapes (attached image). It shows that the two peaks left and right from the GABA field are not just Glu and Gln. You can see that the peak around 3.7ppm is a mixture of Glu, Gln and GSH whereas the peak around 2.3ppm is a sum of Glu, Gln and GABA. Therefore the GLX peaks given by TARQUIN might be biased by GSH and GABA contributions.

But as Martin said there is probably nothing wrong with getting your Glx values from either, but because of the above reason I'd stick with the OFF spectra.

best wishes

Felix

[Paul Mullins]

Hi all,

For my two bits - the issue of co-contamination of Glutamate signal with Glutamine and GSh, while improved, is not one that goes away entirely when using the OFF spectrum as a PRESS acquisition, although if you are a TE of 80, overlap with Glutamine is certainly reduced (some even suggest removed due to J modulation of the Glutamine and Glutamate side peaks).  However there is a more practical reason I would prefer to use the OFF spectrum and that is due to slight inconsistencies of saturation/subtraction around 1.9 ppm.  I know we all get really great spectra from MEGA-PRESS all the time* with lovely flat baselines, but if I ever do see funky things happening in my spectrum it usually happens around the 2.3 - 1.7 ppm region.  This doesn’t happen all the time, but enough to make me wary of measures in this region.  Of course you could just use the sum of the peaks at 3.7 ppm, as some researchers do using LC-Model, but I would also use the OFF spectrum as a sanity check.  You are likely going to fit the OFF spectrum anyhow to get NAA, Cho and Cre, so it’s not like it will be a huge extra step.

Felix, thanks for the link to the LC-Model basis set, I shall investigate that.

Cheers

Paul. 

* and by all the time I mean every time we get usable data, as always, your milage may vary. ;-)

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<Glx_MP.png>

 

Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office.

[caroline...@gmail.com]

Dear all, 

Thank you so much for these quick and incredibly helpful responses.  It sounds like there is an abundance of evidence in favor of using the OFF spectra, which I am relieved to hear and will use to motivate my analysis going forward.  I'm looking forward to having a look at the simulated basis set as well.  

Thank you all again!

Caroline

Hi all,

<Glx_MP.png>

[harshal patel]

Dear all,

First of all, thank you  Martin for developing TARQUIN and  for discussing Glx quantification using MEGA-PRESS OFF spectra.

I would like to quantify glx using OFF spectra. However I am not sure if I am using the correct parameters in TARQUIN. I think some of you must have tried it and hence your Inputs/suggestions on choosing the right parameters in TARQUIN for  off spectra quant. would be very helpful to me.

FYI: I have acquired SVS spectra @3T using MEGA-PRESS sequence with VOI/TE/TR 30mm/68ms/2000ms. I Import off spectra (.rda) as water suppressed data and then import  water unsuppressed (.rda)data in TARQUIN with following parameters.

sampling frequenecy = 2000

TE = 68

Pulse sequence =PRESS

TE1  = 12

CPMG = 10

Dynamic averaging (WS) = No

Dynamic averaging (W) = No

Dynamic frequency correction = disable

Dynamic corr. ref. Signal (WS) = 1h NAA Cr Cho Lip

full echo = disable

swap rows and coloum = disable

water cutoff(Hz)  = 45

Convolution width(pts) = 0

reference Offset (ppm) = 4.65

Reference Signal = 1h NAA Cr Cho Lip

Max dref = 0.15

Zero fill K-space factor = 1

Auto Phase = enable

Auto reference = enable

Eddy current correction = disable

Combine preprocessing = disable

Lipid filter = disable

start Point = 20

end Point 2048

Lambda = 0.2

Initial mu = 0.001

Maximum Iteration = 75

Initial Beta= 0

water concentration  = 35880

water attenaution = 0.7

max metabolite shift (ppm)= 0.003 

max broad shift (ppm) = 0.1

internal Basis set 1H brain + Glth

Zero filling = 2

right ppm Limit = 0.2

left ppm Limit = 4

baseline smoothing Point = 25

line broading (hz) = 0

with no external Basis set.

Is it okay to go further with the above mentioned parameters to quantify glx using off spectra?? I just want to be sure before i run TARQUIN over the off spectra.

Thank you very much in advance.

Best

Harshal

 Thank you Martin for developing this great tool (Tarquin), and all for the helpful discussion on resolving Glx in MEGA-PRESS spectra.

[Martin Wilson]

Hi Harshal,

As a general strategy, I would keep everything as default and fit a few spectra. If the results look ok then carry on and fit the rest. If not, send us an example of a poor result and it may be possible to tweak the defaults to improve things slightly.

Martin

Hi all,

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<Glx_MP.png>

 

Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office.

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